sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0c3b72b69912b21d5a4312ad0541a13bcb97b04bd6b959c13383936817a97a85 | MATLAB | 10,773 | 269 | function hText = xticklabel_rotate(XTick,rot,varargin)
%hText = xticklabel_rotate(XTick,rot,XTickLabel,varargin) Rotate XTickLabel
%
% Syntax: xticklabel_rotate
%
% Input:
% {opt} XTick - vector array of XTick positions & values (numeric)
% uses current XTick values o... |
84f34abaf86dbae5814a0a1b3580b141a8624831ddb4d6d805ea6367387b64c8 | MATLAB | 10,775 | 231 | function [Signal_time] = SignalModelR2_Submission(D_axons,V_Fiber,G_axons,params)
% This function estimates the averaged signal in an unitary voxel with a
% specific amount of axons aiming to specific directions (D_axons), with
% specific volume (V_axons) and G ratio (G_axons) dispersed with a specific
% Watson ... |
d4b1994477214137cc9e9b6148c24150559264e818df61be91eb456c6b9da27d | MATLAB | 10,955 | 226 | function [crp_parms, crp_projs]=CRP_method(V,t_win)
% function [crp_parms, crp_projs]=CRP_method(V,t_win)
%
% This function performs canonical response parameterization
%
%
% Input variables:
%
% V: single-trial stimulation-evoked voltage matrix (Dimensions of V are
% T×K, with T total timepoints by K tota... |
cfebbed95b086372451e183b966e094255ada2286b5cfe91cc34804dfa1d76e4 | MATLAB | 11,002 | 246 | function [corr_db, mdata] = gather_correlation_statists(db)
% Function gather_correlation_statists() produces flat db from a db of a single experiment,
% as produced by the pipeline.
%
% Inputs:
% db - (struct) - The db that holds the complex datastructure, as in db_h.data of the
% ... |
6efefd79e81e6373d6105155fe0a075e64cddbb0ed0493056e6e2aea260072db | MATLAB | 11,030 | 263 | %---------------------------------------------------------------%
% This is the main script for calculating INSeq vs. OUTSeq %
% trajectory distance in the original state space. %
% -- Wenbo Tang (Jan 07, 2023) %
%-------------------------------------------------------... |
893c3982ebc34b34ba6ad24ebf5d9d5e9e3f22a2e8313f06c3e6109e0d822c7f | MATLAB | 11,062 | 200 | function y_est = MIRO_Fast_Wiener(z, y_hat, sigma, smp)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This algorithm is adapted from the article:
%
% [1] K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, "Image Denoising
% by Sparse 3D Transform-Domain Collaborative Filtering," ... |
62861832df5c0e855cce500c4cc883ce2cf433eae3be34349d228d295f492d28 | MATLAB | 11,090 | 277 | % ============= Opening functions =======================
function varargout = rat_direction_labeler(varargin)
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @rat_direction_labeler_OpeningFcn, ...
... |
fdf949e615e027676b02ba77fcd18076f1411ffa038a11d5ec249f88730109e7 | MATLAB | 11,090 | 263 |
%% MAIN MASTER: NEURODEGENERATION CODE
% Written: ASC + ZK
% Date: 2022-04-27
% Updated: 2022-01-26
% Main script for AUDDIT
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Initialization and user input
close all
clear;
clc;
% Add path of code location (CHANGE TO WHERE IMA... |
6dc28480648b2f3785d6c5e2b0c40b1a41cbf5d64294084df3d81ee04a39ae02 | MATLAB | 11,102 | 406 |
function varargout = FinchScopeMk3(varargin)
% FinchScope DAQ software.
% WALIII
% d02.09.15
%
% NOTE: before starting, you will need to identify that both the camera,
% and arduino are recognized by matlab. This can be done with the comand:
% >> imaqhwingo % for the camera
% >>
%
%
%
%
gui_Singleton = 1;
gui_Stat... |
2a745b3b784fd57ea4471649e4f46a70b9343ec4db16f3deff7c262895b215e6 | MATLAB | 11,116 | 151 | %% LaBGAS_get_firstlvl_dsgn_obj_pmods
%
% This script contains a function that defines a number of fields of
% the CANlab style first level DSGN structure array
% for Maaike's emosymp study on IAPS picture-induced bodily symptoms,
% including parametric modulators.
% This function is used in LaBGAS_1_spm_fit_firstlvl... |
d77558895bf868ba6d504eb6ff6cdc3a1b004753577f103e6980909b89ef3c50 | MATLAB | 11,128 | 166 | % ClinicalASL toolbox 2023, JCWSiero
%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 25-05-2023 for the MOYAMOYA study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smoot... |
7843b46239e90db198fb66216ce25b582669744db24fc068e690560709756fd7 | MATLAB | 11,280 | 366 | function saveastiff(data, path, options)
%% usage： saveastiff(im2uint16(yourfile/max(:), double type), 'yourfile.tiff')
% options.color
% : true or FALSE
% : If this is true, third dimension should be 3 and the data is saved as a color image.
% options.comp
% : 'no', 'lzw', 'jpeg' or 'adobe'.
% Compression t... |
4572e6fa91bbc1c27f0214f5859f699e12bb0f0d6f44b96a8c0287c02d132ea3 | MATLAB | 11,326 | 205 | %Authors: Tatjana Schmitt & Simon Wadle, 2019-2022
% based on concepts published in Romero et al. (2019): Cellular and Widefield Imaging of Sound Frequency Organization in Primary and Higher Order Fields of the Mouse Auditory Cortex. Cerebral Cortex 30: 1603-1622
%requieres Matlab packages chronux_2_12 (info : ht... |
84c97ad3bc8a52c6ef12b89d1db6a3178562992faabfc04f4f03c41b6c33b9fa | MATLAB | 11,328 | 274 | %---------------------------------------------------------------%
% This is the main script for calculating the distance of %
% neural states between N' and shuffled neural activity in the %
% original state space. -- Wenbo Tang (Jan 07, 2023) %
%------------------------------------------------------... |
cbe40d0b29dffa28c63b40430a90319c13612c7b348bb89034008f51af7c799c | MATLAB | 11,503 | 396 | function IDX = IDXforbmcBRFS2021
%% load session data
global STIMDIR
cd(STIMDIR)
didir = strcat(STIMDIR,'\');
saveName = 'IDXforIOTana';
anaType = '_MUA_old.mat';
flag_saveIDX = true;
saveYourFigs = true;
kls = 0;
list = dir([didir '*' anaType]);
sdfwin = [-0.15 .8];
clear holder IDX
SupraCount = 0;
Gra... |
78f8f70b827b4c9c740c3b1bd3fd639119c4f40e7daf6ca04d35c60f0c928be3 | MATLAB | 11,542 | 268 | %---------------------------------------------------------------%
% This is the main script for calculating the distance of %
% neural states between N' and shuffled neural manifolds. %
% The UMAP MATLAB toolbox (V4.1) is needed (https://www. %
% mathworks.com/matlabcentral/fileexchange/ ... |
8439a96152dec39b01d62f4774ab4031169602174b3094cf6ee3a92de92ad8f3 | MATLAB | 11,554 | 270 | %Author: Tatjana Schmitt, 2019-2022
clearvars
%% set parameter
save_flag = true;
% objective parameter
wf_objective = '10x'; % either '10x' or '4x'
imaging_objective = '16x'; % either '16x' or '20x'
if strcmp(imaging_objective, '16x')
pixel_size = 1.602;
elseif strcmp(imaging_objective... |
46243df7b290683f5fa17a7360a70619f663b863c2f9291e546d5110ba023282 | MATLAB | 11,645 | 212 | %% About this script
%
% Optional: Run these load and attach behavioral data from files (e.g., from Excel)
%
% This script is an example script only. You should modify it to fit your
% needs, which will depend on which types of behavioral/non-imaging data
% you have and what variables you want to store and... |
e33c7834107050097edab95601d836628449a1d332fe35da632531503467cc66 | MATLAB | 11,824 | 256 | function [imLocCont,imFeatures,imDend,imOrigBig] = findBlebs(imOrig,sFactor)
close all
% Get background standard deviation
t = adaptthresh(imOrig,.2);
imbw = imbinarize(imOrig,t);
imNot = ~imbw;
bkStd = std2(imOrig(imNot));
% Local contrast adjust cropped image.
%... |
63791381d0a849d7aac0221a273d05fe04c0a9211eadf21d0881be05c3acb1df | MATLAB | 11,835 | 275 | %---------------------------------------------------------------%
% This is the main script for calculating INSeq vs. OUTSeq %
% trajectory distance based on UMAP manifolds of neural %
% population activity. The UMAP MATLAB toolbox (V4.1) is %
% needed (https://www.mathworks.com/matlabcentral/filee... |
dd4081c4656b358573a6d51635bd835ea001794996ae3dbaa37870649467c7d3 | MATLAB | 11,994 | 376 | function implement_MDP
% Initialize hardware connections
% Set initial state
% Main loop:
% observe animal - position and action
% as a function of current state and animal state, select action
% as a function of current state and animal state, select next state
%
% Animal state: x, y and nose poke state
% MDP st... |
69f50abdaa38b36186e2cb3b43b5086f908fc14af9590f3478e65bd230fbf3f2 | MATLAB | 12,006 | 303 | function res = saveastiff(data, path, options)
% options.color
% : true or FALSE
% : If this is true, third dimension should be 3 and the data is saved as a color image.
% options.compress
% : 'no', 'lzw', 'jpeg' or 'adobe'.
% Compression type.
% 'no' : Uncompressed(Default)
% 'lzw' : lossles... |
d3b748bcbdb2d119382e4d97a950b09ea75c7649c9a07d07c02a33033efd9f42 | MATLAB | 12,010 | 322 |
% breakyaxes splits data in an axes so that data is in a low and high pane.
%
% breakYAxes(splitYLim) splitYLim is a 2 element vector containing a range
% of y values from splitYLim(1) to splitYLim(2) to remove from the axes.
% They must be within the current yLimis of the axes.
%
% breakYAxes(splitYLim... |
845748791f56c1916c327247a70e83a484873bf96a2d33795d1e2b50b9066fd2 | MATLAB | 12,042 | 373 | function X = diUnitTuning_BRFS(RESP,STIM,brfsfiles)
X = [];
if ~isequal(size(STIM.eye),size(RESP))
error('pass resp for 1 channel and 1 window only')
end
if all(isnan(RESP))
return
end
% Determin Neuron's Orientation Tuning
clear I varnames
I = (STIM.monocular | STIM.dioptic) ...
& STIM.adapted == 0 ..... |
9d452e5c95ec71fc3c6a0d9af87c6066d38a2444bca74c7f09cb471857d74744 | MATLAB | 12,071 | 368 | function X = diUnitTuning(RESP,STIM,goodfiles)
X = [];
if ~isequal(size(STIM.eye),size(RESP))
error('pass resp for 1 channel and 1 window only')
end
if all(isnan(RESP))
return
end
if nargin < 3 || isempty(goodfiles)
goodfiles = unique(STIM.filen);
end
% Determin Neuron's Orientation Tuning
clear I varna... |
f2edebd1119acade7dba400fb318311ec46afd50b02fc518f6b0299c1f15a21a | MATLAB | 12,248 | 364 | function [C,numberOfOverlapPixels] = normxcorr2_general_freq(varargin)
%NORMXCORR2_GENERAL Normalized two-dimensional cross-correlation.
% [C,numberOfOverlapPixels] = NORMXCORR2_GENERAL(TEMPLATE,A) computes the
% normalized cross-correlation of matrices TEMPLATE and A. The resulting
% matrix C contains correlatio... |
0c6b343784eae306dd95ee634a592847f94f30005cda5f1d67d6a4ceba4fb895 | MATLAB | 12,270 | 216 | %% Figure 2
measure = 'envCorrDBTorth_gamma';
ephysMeasures = {'envCorrDBTorth_highGamma','envCorrDBTorth_gamma','envCorrDBTorth_beta','envCorrDBTorth_alpha','envCorrDBTorth_theta','wPLI_dbt_beta','wPLI_dbt_alpha','wPLI_dbt_theta'};
RSdata = loadReportDate([getLocalPath('ECoGoutput') 'Embeddings' filesep 'RSda... |
e9014477313e4db35bcd87f286b3321491134ef7cde644db8b0082b2f67dfe88 | MATLAB | 12,278 | 328 | function camera_parser_module_mat_to_pdf(db, out_folder)
% JN 2019-01-28 added saving in `out_folder`, made figures invisible
% Function camera_parser_module_mat_to_pdf generates graphical evaluation of the analysed data from
% the camera. The script produces two figures in .png format.
% Runtime: 4 sec
% Input:
% ... |
1af3ba028ea987c6f9083e7fc6c50ccb758a5107b5709baea887ba90dfdb7809 | MATLAB | 12,323 | 440 | function AUTOdiIDX_monocOccCompare
% Make sure tm goes out to .9 (in time for the second stimuli) Hopefully I
% can crop the extra .1 later if needed. But this should at least show me
% the second peak as a sanity check.
clear
tic
didir = 'T:\diSTIM - adaptdcos&CRF\STIM\';
saveName = 'diIDX_AUTO_monocOccCompare'; % ... |
5558e1b4b2564ee3ffa365313b328e3a0f1d85b1f13d0cd88b5a5556424176e8 | MATLAB | 12,432 | 407 | function AUTOdiIDX_RESPonly_equiocularIncluded
% Make sure tm goes out to .9 (in time for the second stimuli) Hopefully I
% can crop the extra .1 later if needed. But this should at least show me
% the second peak as a sanity check.
clear
tic
didir = 'T:\diSTIM - adaptdcos&CRF\STIM\';
saveName = 'AUTOdiIDX_RESPonly_... |
5f4d42b48e3b042b2751bbc8413773f7c209bf300dea918bc7b993dd980cab6d | MATLAB | 12,547 | 347 | IDX = IDX_iScienceSubmission
%% load session data
global STIMDIR
cd(STIMDIR)
didir = strcat(STIMDIR,'\');
saveName = 'IDX_iScienceSubmission.mat'; % THIS IS CONTRAST LEVELS OF .41-.75 INCLUSIVE
anaType = '_AUTO.mat';
flag_saveIDX = true;
kls = 0;
list = dir([didir '*' anaType]);
sdfwin = [-0.05 .9];
clea... |
cb252b1ec623bc7ea368b2a79f89b214c452ce9471bb93fbd6ad1c254c668476 | MATLAB | 12,593 | 408 | function AUTOdiIDX_RESPonly_AllTMandAdaptedEffect
% Make sure tm goes out to .9 (in time for the second stimuli) Hopefully I
% can crop the extra .1 later if needed. But this should at least show me
% the second peak as a sanity check.
clear
tic
didir = 'T:\diSTIM - adaptdcos&CRF\STIM\';
saveName = 'AUTOdiIDX_RESPon... |
b0203094d693245942403ea1bc6d6cacba040a74ebbfdea3bda971f0e85e06a3 | MATLAB | 12,620 | 361 | function [Y,ndx,dbg] = natsort(X,rgx,varargin)
% Natural-order / alphanumeric sort strings or character vectors or categorical.
%
% (c) 2012-2021 Stephen Cobeldick
%
% Sorts text by character code and by number value. By default matches
% integer substrings and performs a case-insensitive ascending sort.
% Options sele... |
e128d69afd88e0a42a79b569e5e47a7d2ca9367b8f0c04afb6c305cde7744c9c | MATLAB | 12,622 | 428 | function [IDX,ERR] = IDX_iScienceSubmission(ROOTDIR)
% This function loads in event-triggered data, establishes unit
% preferences, and then sorts condition types from the perspective of the
% individual multi-unit's tuning.
anaType = '_AUTO.mat';
list = dir([ROOTDIR '*' anaType]);
sdfwin = [-0.05 .9];
clear ... |
2ba8e3ee2b2fd91caef2cb0d188b13bdbed0e7b50acfb4be5290bd2db72688b8 | MATLAB | 12,810 | 326 | filePath = '\\ODIN\p\graham_preprocessing\importnat_data_from_graham\';
subjects = {'369','372','376','400','405','409','418','423','456','460'};
ROIsToUse = {'OG','PHG','STGM','TFG','PP','PT','ITGP','SPL','vPostCG','TP','IFGor','GR','ITGA','STGA','MOG','IFGop','PMC','STSL','STGP','SMG',...
'dPreCG','CingM',... |
2b233dc6fcb05a37f0421f12ddc9f903f0bfb6389038eeadd240dcb34a047917 | MATLAB | 12,825 | 384 | function [n_signif,index_signif] = fdr(pvals,qlevel,method,adjustment_method,adjustment_args)
%
% Attribution:
%
% Version 0.1.3; May 10, 2004
%
% License: GPL version 2 or later
%
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as p... |
2dabdb5ebc5a7c79ba5735e7461ba1216ba05ec1f35c1f6ce148332e059a857c | MATLAB | 12,903 | 296 | function mdp_analysis_nightRIFF(sounds_table, mdp_table, outputdir)
if sum(mdp_table.type == 'playSound')
%sounds played in session
pSi = find(mdp_table.type == 'playSound');
pSii = find(diff(pSi) > 1);
pSarea = mdp_table.s_area(pSi(pSii)+1);
fig = figure('Position', [0 0 1000 800], 'Visible', 'off... |
7d3fdf2cd49b14feb6a27c3eecce3743c679230564d1e83e29658b01af0e9437 | MATLAB | 12,923 | 308 | %---------------------------------------------------------------%
% This is the main script for calculating the distance of %
% neural states between N' and F in the the original state %
% space -- Wenbo Tang (Jan 07, 2023) %
%-------------------------------------------------------... |
cb210d59c0e0c0fe74333074c052d6e0e6213f88b0dd12faca097594cb1e59f4 | MATLAB | 12,947 | 437 | function [h0, h1] = dfilters(fname, type)
% DFILTERS Generate directional 2D filters
%
% [h0, h1] = dfilters(fname, type)
%
% Input:
% fname: Filter name. Available 'fname' are:
% 'haar': the "Haar" filters
% 'vk': McClellan transformed of the filter from
% the VK book
% 'ko': orthogonal filter in the Kov... |
b50382cba94ab2ac51852d4b607362474191e9e199471e954434516038839b3e | MATLAB | 12,988 | 433 | %% HouseKeeping
clear; close all
addpath('D:\Documents\Software\spm12\PublicVersion');
spm('defaults', 'eeg')
addpath('D:\Documents\Software\FIL-OPMEG\OPM');
addpath('D:\Documents\Software\linspecer');
addpath('D:\Documents\Software\export_fig');
%% Config
resultsSavePath = '.\EnvironmentalNoise\results';
rawDataPath... |
fed76ee0505ebec7059982d09b504fe91861362d3d162db1c5225c1b7768049f | MATLAB | 13,088 | 443 | % Mean firing rate in the time window from spike latency to 100ms
% bar graphs in Fig. 2, a-c
clear; clc; close all;
% load spike data
load('spikes.mat');
%% Monkey A
% Firing rate
b1c100 = mSpikes_A_b1c100; % wide-prior, high contrast
b2c100 = mSpikes_A_b2c100; % narrow-prior, high contrast
b1c008 = mSpikes_A_b1c0... |
62b87ecd0160383f4e694afb027998ff1c568f6a4ac887d88bcdb045b6be34ca | MATLAB | 13,114 | 251 | % This script describes the statistical analysis of age effects on MEG power and connectivity as well as cortical thickness.
% Steps for visulatization of the results are described and are partially done using Matlab or R.
%
% Christina Stier 2022
%% Vertex-wise analysis using PALM (https://fsl.fmrib.ox.ac.uk/fsl/fs... |
459d755b5773744c0a7c17481d5e81f0ca5d106b7573194f2b1ce91471ce7811 | MATLAB | 13,117 | 314 | classdef CocoApi
% Interface for accessing the Microsoft COCO dataset.
%
% Microsoft COCO is a large image dataset designed for object detection,
% segmentation, and caption generation. CocoApi.m is a Matlab API that
% assists in loading, parsing and visualizing the annotations in COCO.
% Please visit http:... |
ea5b331a472d39f1cbb0a1cab79953b5a977b0fa86f16a7ce4ea6f0b0251c407 | MATLAB | 13,136 | 327 | %analysis parameter definitions, to be used for all subjects in this stream
% This is a unified configuaration file for EEG (EGI 256) und MEG
params=[];
% Directory that has the mapping functions for dataset detection
params.dataset_mapping_dir='conf/dataset-mapping';
% -------------------------------------------... |
5e22ed8f65e6b3570756fd8e67085a1181e3f8ab35d87f1b4da1000752ef9a45 | MATLAB | 13,233 | 444 | function IDX = IDX_iScienceSubmission_onlyE48
%% load session data
saveName = 'IDX_iScienceSubmission_onlyE48.mat'; % THIS IS CONTRAST LEVELS OF .41-.75 INCLUSIVE
flag_saveIDX = true;
global STIMDIR
cd(STIMDIR)
list = dir(['*_E_*','AUTO.mat']);
anaType = '_AUTO.mat';
sdfwin = [-0.05 .9];
clear holder ID... |
d43c4241bfbdd420c45f4d5eb2c5eb74714325bf132fabaff0a7c58f46ce1dcc | MATLAB | 13,233 | 444 | function IDX = IDX_iScienceSubmission_onlyI34
%% load session data
saveName = 'IDX_iScienceSubmission_onlyI34.mat'; % THIS IS CONTRAST LEVELS OF .41-.75 INCLUSIVE
flag_saveIDX = true;
global STIMDIR
cd(STIMDIR)
list = dir(['*_I_*','AUTO.mat']);
anaType = '_AUTO.mat';
sdfwin = [-0.05 .9];
clear holder ID... |
5656e36f7bfd115703377f09c93f5a9b7b196dd2c6c8f7830a7f599dd243ed0b | MATLAB | 13,257 | 368 | function [Y,ndx,dbg] = natsort(X,rgx,varargin)
% Natural-order / alphanumeric sort strings or character vectors or categorical.
%
% (c) 2012-2021 Stephen Cobeldick
%
% Sorts text by character code and by number value. By default matches
% integer substrings and performs a case-insensitive ascending sort.
% Optio... |
1bfae124292c0c2af992085aaf8939f85929c71d41d25dc54a7a6ec9b5745f2d | MATLAB | 13,406 | 387 | function [y_est, sigma_est] = bm4d(z, distribution, sigma, profile, do_wiener, verbose)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% BM4D is an algorithm for attenuation of Gaussian or Rician noise in
% volumetric data. This algorithm reproduces the results from the articles:
%
% ... |
57a3d740d5dea8e0ebb846f68111e16bb873d7c6e4a89798a4f8e0feb9da9112 | MATLAB | 13,445 | 465 | function [D, movement_data, feedback_applied, saturated_frames, beep_start_stop] = ...
preprocess_feedback_ERF(raw_data_filepath_root, analysed_data_path, results_save_path, MRI_file_name, subject, session, task, run, varargin)
% Preprocess auditory ERF data for feedback experiment.
% Steps:
% load data,
% re... |
baadfce7e6af4e707d755f235c555e0a789c2c590b5bae8b4920a0117f679ac8 | MATLAB | 13,513 | 446 | function IDX = IDX_iScienceSubmission_unbalancedContrast
%% load session data
global STIMDIR
cd(STIMDIR)
didir = strcat(STIMDIR,'\');
saveName = 'IDX_iScienceSubmission_unbalancedContrast.mat'; % THIS IS CONTRAST LEVELS OF .41-.75 INCLUSIVE
anaType = '_AUTO.mat';
flag_saveIDX = true;
kls = 0;
list = dir([did... |
829e9efe4c6bc17a0b014e9818ce085711840f01eb959c1b7681f1ab43bd459f | MATLAB | 13,550 | 446 | function IDX = IDXforGrammJuly2021;
%% load session data
global STIMDIR
cd(STIMDIR)
didir = strcat(STIMDIR);
saveName = 'test'; % THIS IS CONTRAST LEVELS OF .41-.75 INCLUSIVE
anaType = '_AUTO.mat';
flag_saveIDX = 1;
kls = 0;
list = dir([didir '*' anaType]);
sdfwin = [-0.05 .9];
clear holder IDX
SupraCoun... |
11957b63ce8a47898037059c1970a19fd351755d9debe1393f9917febdbc2031 | MATLAB | 13,575 | 387 | % direction, speed, latency of smooth pursuit eye movements for prior direction
% Fig. 1 d,e and fig. S1 c-f
clear; clc; close all;
% load data
load('behavior.mat');
%% direction
direction = direction_day_prior_A;
% direction_prior_day_A: prior direction, monkey A, for each day
% direction_prior_day_B: p... |
4d9868321babf655893251043b2abccc76b1e598cc85e4da038ef6b2ad2a3e91 | MATLAB | 13,644 | 270 | %Author: Tatjana Schmitt 2019-2022
function FRA_analysis_combine_awake_redcell(root_path)
save_flag = true;
%% matrices
Rsquare_red = zeros;
Rsquare_green = zeros;
FWHM_1_red = zeros;
FWHM_1_green = zeros;
FWHM_2_red = zeros;
FWHM_2_green = zeros;
all_BFs_red = zeros;
all_BFs_green = zeros;
BF_single_peak... |
6055780dd9ca46e7094f816b2d425bfdb6ee0a1aa5fa8d6164f25d25c7a3dfe5 | MATLAB | 13,647 | 402 | function GLM_stLevel(subID)
% compute first level model contrasts reward-control
% no PM -> covariate 2nd level
% dbstop if error
%% define experiment setting parameters
subj = subID; % to run on server
%% What to do
firstLevel = 0;
constrasts = 1;
copycontrasts = 1;
%% define task variable
sessionX... |
49d00ba373bd911320661ce6297602c7fa229b078be3d0ecd7073af4aae16893 | MATLAB | 13,857 | 444 | function varargout=gui_msgbox(varargin)
%MSGBOX Message box.
% msgbox(Message) creates a message box that automatically wraps
% Message to fit an appropriately sized Figure. Message is a string
% vector, string matrix or cell array.
%
% msgbox(Message,Title) specifies the title of the message box.
%
% msgbox... |
458076f6d581ccfd4df028ff57f4a8fabf14b744e59c229af2f292ca3fe64109 | MATLAB | 13,881 | 474 | function varargout=notBoxPlot(y,x,varargin)
% notBoxPlot - Doesn't plot box plots!
%
% function notBoxPlot(y,x,'Param1',val1,'Param2',val2,...)
%
%
% Purpose
% An alternative to a box plot, where the focus is on showing raw
% data. Plots columns of y as different groups located at points
% along the x axis defined by t... |
7b4a9e7885ae2f29a8c007146254735b3a3a120e8a2306c7f9db99b13c110ea3 | MATLAB | 13,886 | 443 | function [IDX,ERR,pValue,effect] = findPValueDistribution()
%% load session data
global STIMDIR
cd(STIMDIR)
didir = strcat(STIMDIR,'\');
anaType = '_AUTO.mat';
flag_saveIDX = true;
kls = 0;
list = dir([didir '*' anaType]);
sdfwin = [-0.05 .9];
clear holder IDX
SupraCount = 0;
GranularCount = 0;
InfraCoun... |
d06d4f40208ec120c3f1c7cf692331ca7416878bbd345c6e98d12bc8248e3a0b | MATLAB | 13,921 | 486 | %%
%% Paths
clear all;
close all;
% TDR path
tdrDir = '/Users/jeongjunpark/Desktop/Joonyeol/Mante';
addpath(fullfile(tdrDir,'TDR'));
addpath(fullfile(tdrDir,'TDR','nansuite'));
addpath(fullfile(tdrDir,'TDR','tools'));
%% Load data
% Data directory
datadir = fullfile(tdrDir,'/TDR/PFC data 1a');
% datadir = fullfi... |
f90cf7cbf9fa5f63134f71261d87a56f584ed1b4260f90a98a069b57619f7e6d | MATLAB | 13,952 | 414 | %%% This script contains all single subject preprocessing steps
%%% of CamCAN-data (resting-state, maxfiltered)
% written by Christina Stier, 2020/2022
%% Load full list of CamCAN subjects
subjlist = importdata('participants.tsv');
subjects = subjlist.textdata(2:end,1);
%% Selection of subjects
% Either use all su... |
ee03869134c5ef60d17d13de81bf9bc722d0c149317eded2f7b117a7514bcdc1 | MATLAB | 14,166 | 457 | function AUTOdiIDX_160108allCond
% taken from diIDX_May27
% AUTODdiIDX can be found in "Event-alignment fuctions."
% It takes all STIM_AUTO.mat inputs, finds relevant conditions, makes sure
% the contact is tuned, and then saves results in a diIDX matrix which is
% stored locally on HDD D:\5 diIDX dir. Note that all... |
fa6d79032526fc13ba6214e871520bd8b34502169af198b9aa661aff0e4220fa | MATLAB | 14,280 | 452 | function SeparateAxes(varargin)
% SeparateAxes - FUNCTION Push apart axes on a figure, around the origin
%
% Usage: SeparateAxes
% SeparateAxes(..., hAxis)
% SeparateAxes(..., fProportion)
% SeparateAxes(..., 'on')
% SeparateAxes(..., 'off')
%
% SeparateAxes provides a visual "improvement" ... |
b9c191526b28f5f75adcadddf3671fd90fc3e5654cbcf7911f300d1e79e881d2 | MATLAB | 14,331 | 332 | %---------------------------------------------------------------%
% This is the main script for calculating the distance of %
% neural states between N' and F neural manifolds. %
% The UMAP MATLAB toolbox (V4.1) is needed (https://www. %
% mathworks.com/matlabcentral/fileexchange/ ... |
a7818d74a94535632d9faef5717bc9b79ceb56fc2fd247e16554cecdb692c205 | MATLAB | 14,344 | 269 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% --------------- supporting functions ----------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%----------------- Leaky accumulation ---------------------------
function [err, simdat, pred, DecValue] = NID... |
6deb1dabc875974ff2962bdb2962afb0a5f85b6d91533915aeb489ca78b6f798 | MATLAB | 14,768 | 504 | % Using 3D affine matrix to rotate, translate, scale, reflect and
% shear a 3D image volume. 3D image volume is represented by a 3D
% matrix, and data type can be real integer or floating-point.
%
% Usage: [new_img new_M] = ...
% affine3d(old_img, old_M, [method], [voxel_size], [bg], [verbose]);
%
% old_img... |
f9acf6b986d0fd98755b2e9e52928179683e07e35698ba5ddf2e7dc7d4678d3e | MATLAB | 15,068 | 492 | function AUTOdiIDX_halfTM_MedMedC_Untuned
% Make sure tm goes out to .9 (in time for the second stimuli) Hopefully I
% can crop the extra .1 later if needed. But this should at least show me
% the second peak as a sanity check.
clear
tic
didir = 'T:\diSTIM - adaptdcos&CRF\STIM\';
saveName = 'diIDX_AUTO_halfTM_MedMed... |
1e405af076cb7ce309afa89adf82c2f504a7f122b8cc1ea3211c316b88d20aa3 | MATLAB | 15,088 | 497 | function AUTOdiIDX_halfTM_MedMedC
% Make sure tm goes out to .9 (in time for the second stimuli) Hopefully I
% can crop the extra .1 later if needed. But this should at least show me
% the second peak as a sanity check.
clear
tic
didir = 'T:\diSTIM - adaptdcos&CRF\STIM\';
saveName = 'diIDX_AUTO_halfTM_MedMedC'; % TH... |
2768431ab2e3ab9ffe557ae316ade03362adbdd8f3e759cd9674f8931c926040 | MATLAB | 15,157 | 356 | function varargout = ionpathtracker_gui(varargin)
% IONPATHTRACKER_GUI MATLAB code for ionpathtracker_gui.fig
% IONPATHTRACKER_GUI, by itself, creates a new IONPATHTRACKER_GUI or raises the existing
% singleton*.
%
% H = IONPATHTRACKER_GUI returns the handle to a new IONPATHTRACKER_GUI or the handle to
%... |
9a1cb512e7457608462e20d208176872f3e776c54f1876629ea100da917322e0 | MATLAB | 15,157 | 328 | % Neuromag layout of whole channels
% This function returns the positions of 306 MEG channels
% Copyright by Hong Gi Yeom
% You can use this code for academic purposes
function [position]=neuromag_layout_all()
p=[
1 -73.416206 33.416687 5.000000 4.800000 0113
2 -73.416206 38.416687 5.000000 4.800000 0112
3 -67.416206... |
32ebbfa78193d8db15d894411be542bdff69454397d1bb95ea7f2d3c3c5efa00 | MATLAB | 15,177 | 289 | %DAWN Black-purple-blue-green-yellow-white colormap
%
% Examples:
% map = dawn;
% map = dawn(len);
% B = dawn(A);
% B = dawn(A, lims);
%
% A black to white colormap with several distinct pastel shades reminiscent
% of colors at dawn. This colormap has been designed to achieve perceptual
% uniformity.... |
a86a1f3c2c012dcb5d1599d019b3544f11d44c4d0773616bf1e167cf17f0dca3 | MATLAB | 15,354 | 506 | function AUTOdiIDX_fullTM_MedMedC
% taken from diIDX_May27
% AUTODdiIDX can be found in "Event-alignment fuctions."
% It takes all STIM_AUTO.mat inputs, finds relevant conditions, makes sure
% the contact is tuned, and then saves results in a diIDX matrix which is
% stored locally on HDD D:\5 diIDX dir. Note that al... |
b328638378544cfb8e1a14218354ef72b0b5474b6f6189527aecb3027732ca98 | MATLAB | 15,360 | 506 | function AUTOdiIDX_MediumMediumContrast
% taken from diIDX_May27
% AUTODdiIDX can be found in "Event-alignment fuctions."
% It takes all STIM_AUTO.mat inputs, finds relevant conditions, makes sure
% the contact is tuned, and then saves results in a diIDX matrix which is
% stored locally on HDD D:\5 diIDX dir. Note t... |
e9b3c92c205fef5a8e639a3fc09449df35080afd45c0276969a66c1cde74484f | MATLAB | 15,478 | 372 | %% How to Run This Code
% Run sections #1 and #2
% (Optional) For checking other parameters, run section #3
%%
clc
clear
close all
%% #1 Loading Data
% Folder path where the zip file was unzipped
folder_path='C:\Users\Sanghyeon Park\Dropbox (IBS)\CLASS-SMLM Paper\Nature Communications Submission\Resp... |
282c2efa60f03c361f0d02041c4e9f24ac454cdae9d8f87c8b43eacfc6abc76e | MATLAB | 15,534 | 474 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_untouch_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
e... |
0aa86c000f175ed94380b3f2a487f8e2102c2d7d243e8eead5b28dc59f644ca2 | MATLAB | 15,558 | 338 | %% mdw_postprocessing, fourier analysis
clear all,close all,clc
Analysis = 'Fourier';
brain_slices_select = 8:11; %Change here, usually 8:11 slices for whisker
AllData_dir='E:\mouse_development_whisker';
cd(AllData_dir)
age_list = dir('mouse*');
ROIs = ["_SSpbfd" "_Subcortex" "_SS Cortex" "_SSpbfdR"];
for ... |
2d217f3785110019f25aff57766eae84e5d19947e645524197340506c7cf9fe2 | MATLAB | 15,561 | 475 | function varargout = record_gui_synced6(varargin)
% RECORD_GUI_SYNCED6 MATLAB code for record_gui_synced6.fig
% RECORD_GUI_SYNCED6, by itself, creates a new RECORD_GUI_SYNCED6 or raises the existing
% singleton*.
%
% H = RECORD_GUI_SYNCED6 returns the handle to a new RECORD_GUI_SYNCED6 or the handle to
%... |
f9632ecb36f5889f19ddf2c530dcebf268a547cb780b9857535e3b9c100df430 | MATLAB | 15,567 | 533 | % Test LFP spec on MUA trial selection
clear
close all
PostSetup('BrockHome')
flag_SaveFigs = false;
%% load session data
global STIMDIR
cd(STIMDIR)
penetration = '151221_E_eD_LFP.mat';
load(penetration,'STIM')
matobj = matfile(penetration);
%% Establish variables to change
sdfwin = [-0.150 .5];
ConditionToTest = ... |
49fc09f03abd6f5ca65a52c6129b47de321c5e6b181d5c514d61fea171818367 | MATLAB | 15,624 | 326 | %% LaBGAS_1_spm_prep_firstlvl_models
%
% This script generates a CANlab style first level DSGN structure array and
% CANlab/spm style onset/duration and noise regressor files
%
% See canlab_glm_single_subject('dsgninfo'), or documentation in
% Github\CanlabCore\CanlabCore\GLM_Batch_tools for details on first level
% a... |
d3f73de8d279b2dd3c1b274252489857dc319a1413edb1750ad856dc70ffd16e | MATLAB | 15,739 | 516 | function AUTOdiIDX_LowLowContrast
% taken from diIDX_May27
% AUTODdiIDX can be found in "Event-alignment fuctions."
% It takes all STIM_AUTO.mat inputs, finds relevant conditions, makes sure
% the contact is tuned, and then saves results in a diIDX matrix which is
% stored locally on HDD D:\5 diIDX dir. Note that al... |
00bf6abd003bfbb0e6c2e9e5bbd9e46cbb1ed83ddad7a7470042a92ddd0c5bb3 | MATLAB | 15,770 | 401 | %% LaBGAS_run_MVPA_regression_single_trial
%
% This script runs MVPA regression analysis on a continuous outcome Y
% (lasso-pcr, but can easily be adapted to support vector regression or
% other methods available in CANlab's predict function) on an fmri_data_st
% object created using LaBGAS_create_single_trial_fmri_dat... |
188a8887e5e9dd3fb77ddb4a3d55ffd49e51b75ba8effe8dc12b0a5ef873b811 | MATLAB | 15,886 | 486 | % Modifications to original code are Copyright (C) Alex A. Bhogal, 2022, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl. Please see the original license file provided by
% Tong et. al that is included with this code.
%
% <carpetEdgeDetect: performs shag carpet plot analysis and outputs transit maps >
%
% T... |
9530efe409af2f66fd6889086283dc8f94914ba04b156f63f64640fe79d85c6f | MATLAB | 15,917 | 317 | %% LaBGAS_extract_confound_reg_fMRIprep
%
% This script will extract noise regressors from fMRIprep output for
% the emosymp study, including
% a) CSF signal
% b) 24 head motion parameters (six directions, derivatives, and squared
% values)
% c) dummy spike regressors
%
% DEPENDENCIES
% a) CANlab Github repos on your... |
1594302ed2e75782f297bfa200c0a5b0dfb9db522816789cea39512199dcc553 | MATLAB | 16,013 | 514 | function AUTOdiIDX_highContrast
% taken from diIDX_May27
% AUTODdiIDX can be found in "Event-alignment fuctions."
% It takes all STIM_AUTO.mat inputs, finds relevant conditions, makes sure
% the contact is tuned, and then saves results in a diIDX matrix which is
% stored locally on HDD D:\5 diIDX dir. Note that all ... |
0b35548879d728e6c1d395608c64c6f6b4dd874d8264e5a4a81648a6ce4a0a64 | MATLAB | 16,016 | 517 | function AUTOdiIDX_JoVContrast
% taken from diIDX_May27
% AUTODdiIDX can be found in "Event-alignment fuctions."
% It takes all STIM_AUTO.mat inputs, finds relevant conditions, makes sure
% the contact is tuned, and then saves results in a diIDX matrix which is
% stored locally on HDD D:\5 diIDX dir. Note that all t... |
aafbcb8bb81bacbe2f8920e8b5a0b1b282074c061d43ba65c21eb117c7af5e10 | MATLAB | 16,039 | 544 | function hfig = plotslm(slm)
% plotslm: plots a Shape Language Model (slm) or its derivatives
% usage: plotslm(slm)
% usage: hfig = plotslm(slm)
%
%
% arguments: (input)
% slm - slm struct, as returned by slmengine or slmfit,
% or evaluated by slmeval
%
%
% arguments: (output)
% hfig - figure handle. Only retu... |
44027dd0f541aa776fad0b4c3172ad1e1ef350007991a47c665c9b798aa56afb | MATLAB | 16,041 | 385 | function [crp_projs,crp_parms,bad_trials]=CRP_illustration(fname)
%
% This function reproduces all of the figures, etc, from the manuscript
% "Canonical Response Parameterization: Quantifying the structure of
% responses to single-pulse intracranial electrical brain stimulation"
% by Kai J. Miller, et. al., 2022
%
% ... |
61968b02b51959869510b1ff319acafd4cb892fc52c3e27ba65164b7903ff4f0 | MATLAB | 16,388 | 257 | function [ExVivoTable,HistInfo] = ...
AnisotropyBinning_Submission(Angle_Meas,Kappa_Meas,ICVF_Meas,BetaParams,Mask,params)
%ANISOTROPYBINNING Here the beta values are binned anisotropically to
%ensure equal number of "voxels" as a function of angular orientation.
%Several filters are performed.
% This f... |
baa4f1d6b0dd6d54e1dbba694b730c8a0301174d4484587f1a2416b8a11a4d0a | MATLAB | 16,584 | 356 | classdef CocoUtils
% Utility functions for testing and validation of COCO code.
%
% The following utility functions are defined:
% convertPascalGt - Convert ground truth for PASCAL to COCO format.
% convertImageNetGt - Convert ground truth for ImageNet to COCO format.
% convertPascalDt - Convert d... |
49ca9613991e25892a56d6f41652d5a0314bb530e60626f5c5ca86e50c9017a3 | MATLAB | 17,297 | 259 | data.Is = -15000; % [pA/pF] STIMULUS
data.R = 8314; % [mJ/(mol*K)] Ideal gas const.
data.T = 308; % [K] Temp.
data.Cm = 0.05; % [pF] Membrane capacitance
data.F = 96487; % [C/mol] Faraday const
data.RTON... |
a645f48b1948d7c3eec9c286cae0e4fe2f65d5a4f0044e8693a4982edc089575 | MATLAB | 17,347 | 308 | %% General cylinders study
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This code was created to obtain R2* synthetic data for any cylinder
% configuration and be fitted afterwards by R2* signal models.
% The code operates as follows: A set of
% directions (defined by a file or created on... |
83892e94d03b084ffb97d9509fd5dab8e9713fca2f78a25a8a3357f7749b1efa | MATLAB | 17,575 | 318 | %% OC_AnalysisCode
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This code analyses the optic chiasm (OC) data 4D_X27P.nii R2* weighted
% data. This dataset has 16 angular measurements and 16 echo times per each
% angular measurement.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
3312fd76db9786b0b98ed234b6c6b099b433e31bd4ff98f5db22c8d93c6d5818 | MATLAB | 17,724 | 427 | classdef Point < handle
%UNTITLED4 Summary of this class goes here
% Detailed explanation goes here
properties
name
point_path
path_ext
counts
labels
tags
runinfo
% for denoising
int_norm_d
k_values
count_hist
... |
e96a69dd4f42b1302db86c38e43d2051ef5ab15b918031fedb3bbf2a0f3e883b | MATLAB | 18,058 | 561 | %% Support Vector Machine
% Fig. 3d
clear; clc; close all;
% load experimental data
load('Monkeys_cir.mat');
Monkeys = Data;
% simulate the neural data
% gamma parameters of prefer and null response distribution
% high, prefer
hp = Monkeys(1).Tuning_pfnull(1,:);
nanidx = find(isnan(hp));
hp(nanidx) = [];
params1 = ... |
27492efee3137b36dcda0fe9dc1677844ed5fc7d3c9693d1f22cef7eb787ed21 | MATLAB | 18,208 | 266 | function Binarised_Data = AnisotropicBinning_InSilico_fromExVivo(varargin)
%31.08.2020: Small code who creates 4 different figures with the "loaded"
% matlab file. If it is OLS or MLE, it should apply the same principle. But
% it is required that the entire dataset is calculated.
% OLS: (Max TE data (1,3 and 5),(Disp... |
7fc279acd8c55b37c7792842622cd92a7f592640904a632baffaec3fbc6beb7c | MATLAB | 18,950 | 428 | function [fcsdat, fcshdr, fcsdatscaled, fcsdatcomp] = fca_readfcs(filename)
% [fcsdat, fcshdr, fcsdatscaled, fcsdat_comp] = fca_readfcs(filename);
%
%
% Read FCS 2.0 and FCS 3.0 type flow cytometry data file and put the list mode
% parameters to the fcsdat array with the size of [NumOfPar TotalEvents].
% Some ... |
8c5cc34f1e589e45029aa9eca3c382bef33b506a685a38d4c6a37e55a519682a | MATLAB | 19,024 | 723 |
function varargout = FinchScopeMk4(varargin)
% FinchScope DAQ software.
% WALIII
% d05.23.15
%
% NOTE: before starting, you will need to identify that both the camera,
% and arduino are recognized by matlab. This can be done with the comand:
% >> imaqhwinfo % for the camera
% >>
%
%
%
%% INITIALIZE CODE (DO NOT EDI... |
38596832d3cf57bbab3fd38b02675c307c44104a2032e8d76b790ee65eb08ae5 | MATLAB | 19,072 | 573 | % External coil frequency sweep
clear; close all
addpath('D:\Documents\Software\spm12\PublicVersion');
spm('defaults', 'eeg')
addpath(genpath('D:\Documents\Software\FIL-OPMEG\OPM'));
addpath('D:\Documents\Software\linspecer');
addpath('D:\Documents\Software\export_fig');
%% Config
resultsSavePath = '.\ExternalCoils... |
de854a6a92be41aa4473a71ffc8099bbee5fd4866bf09a5c775661de0a22ccc7 | MATLAB | 19,256 | 424 | function [im_dend,imOrig] = findDendrites(img,side,sFactor)
% Purpose: Imports images of neurons and crops to the size that has
% dendrites for future processing (tracking and degradation
% quantification). User chooses which number image gets sent into the
% function.
% Updated: 08-29-2022
%% Step 1: Load and rotate... |
a68cc92e0966e486e388528d48811ecb9ed57d3e988e134945615bc9955d664f | MATLAB | 19,309 | 752 | function FS_TemplateMatch(TEMPLATE,varargin)
%FS_TemplateMatch allows the user to select a song template, and then attempts to find
%matches to the template through a running Euclidean distance score (similar to SAP)
%
% fb_template_match(TEMPLATE,varargin)
%
% TEMPLATE
% template (vector, default: empty, user selects ... |
436fae228f761eb0d7fa0f15675db502eb196937c6ab49dcf0068077ab251254 | MATLAB | 19,336 | 372 | % CREATE_PLOTS manages the update of the created plots in each trial of the
% experiment.
% CREATE_PLOTS(OUT_MANAGER,LINE_TABLES,TRIAL_INDEX) manages the update of
% the created plots with the help of the OUT_MANAGER object (that holds the
% list of created plots and the number of instances of each one of them),
% LIN... |
06d62c8206f4de2b3a06692cf5f218c7fdb6c9e9b4b527c80fd958cec12c5e9c | MATLAB | 19,586 | 382 | % CREATE_PLOTS manages the update of the created plots in each trial of the
% experiment.
% CREATE_PLOTS(OUT_MANAGER,LINE_TABLES,TRIAL_INDEX) manages the update of
% the created plots with the help of the OUT_MANAGER object (that holds the
% list of created plots and the number of instances of each one of them),
% LIN... |
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